Pleural proteins

Of the 265 samples run, 256 passed the default qc performed in the metaboprep package.

For the moment, all 92 measured proteins have been retained for analysis.

See project_metaboprep_qc_report.html for full details

Phenotype information

The below phenotypic information was available on participants:

> tibble [256 × 51] (S3: tbl_df/tbl/data.frame)
>  $ patient.id                                         : chr [1:256] "C66ME" "C72GS" "C76EG" "C86JH" ...
>  $ age                                                : num [1:256] 91 77 82 89 72 32 79 95 43 43 ...
>  $ female                                             : num [1:256] 1 0 1 0 1 0 1 0 1 0 ...
>  $ infect.fct                                         : Factor w/ 3 levels "control","inter",..: 2 3 2 3 2 3 1 3 3 2 ...
>  $ infect.num                                         : num [1:256] 2 3 2 3 2 3 1 3 3 2 ...
>  $ infect.bi                                          : num [1:256] 0 1 0 1 0 1 0 1 1 0 ...
>  $ final.diagnosis.1                                  : chr [1:256] "X/infection/CPPE" "X/infection/utrue" "X/infection/CPPE" "X/infection/utrue" ...
>  $ paired.blood                                       : chr [1:256] "C66ME" "C72GS" "C76EG" "C86JH" ...
>  $ sex                                                : chr [1:256] "Female" "Male" "Female" "Male" ...
>  $ age.at.enrollment                                  : num [1:256] 91 77 82 89 72 32 79 95 43 43 ...
>  $ who.ps                                             : chr [1:256] "2" "4" "2" "4" ...
>  $ co.morbidity.present                               : chr [1:256] "Y" "Y" "Y" "Y" ...
>  $ co.morbidity.list                                  : chr [1:256] "CKD, hypertension" "COPD, IHD, hypertension" "osteoporosis, hypertension" "hypertension, AF, PMR, gilbert's syndrome" ...
>  $ duration.of..symptoms                              : chr [1:256] "0-1 weeks" "4-6 weeks" "2-4 weeks" "1-2 weeks" ...
>  $ septations                                         : chr [1:256] "Not recorded" "Not recorded" "Not recorded" "Not recorded" ...
>  $ loculations                                        : chr [1:256] "Y" "Y" "Y" "Y" ...
>  $ lights.criteria                                    : chr [1:256] "Exudate" "Exudate" "Exudate" "Exudate" ...
>  $ ph                                                 : chr [1:256] "7.45" "7.38" "7.34" "7.0780000000000003" ...
>  $ crp                                                : chr [1:256] "240" "398" "338" "245" ...
>  $ wcc                                                : chr [1:256] "13.5" "15" "18.7" "16.7" ...
>  $ neutrophils                                        : chr [1:256] "11.1" "12.1" "15.9" "15.3" ...
>  $ nlr                                                : chr [1:256] "8.5399999999999991" "5.5" "13.25" "25.5" ...
>  $ pf.culture                                         : chr [1:256] "No growth" "No growth" "No growth" "No growth" ...
>  $ organism.isolated                                  : chr [1:256] "0" "0" "0" "0" ...
>  $ hospital.los                                       : chr [1:256] "26" "15" "20" "20" ...
>  $ chest.drain.insertion                              : chr [1:256] "Y" "Y" "Y" "Y" ...
>  $ lytics                                             : chr [1:256] "N" "N" "N" "N" ...
>  $ surgery                                            : chr [1:256] "N" "N" "Y" "N" ...
>  $ study.enter.date                                   : POSIXct[1:256], format: "2009-08-03" "2009-08-10" ...
>  $ death.date                                         : chr [1:256] "43131" "40069" "41011" "40067" ...
>  $ mortality..3m.                                     : num [1:256] 0 1 0 1 0 0 0 0 0 0 ...
>  $ mortality..1yr.                                    : num [1:256] 0 1 0 1 0 0 0 0 0 0 ...
>  $ composite.outcome..lytics..surgery.or..3m.mortality: num [1:256] 0 1 1 1 0 0 0 0 0 0 ...
>  $ notes                                              : chr [1:256] NA NA NA NA ...
>  $ product                                            : chr [1:256] "TARGET96" "TARGET96" "TARGET96" "TARGET96" ...
>  $ panelversion                                       : int [1:256] 3028 3028 3028 3028 3028 3028 3028 3028 3028 3028 ...
>  $ plateid                                            : chr [1:256] "GB390725-RB_1" "GB390725-RB_1" "GB390725-RB_2" "GB390725-RB_2" ...
>  $ wellid                                             : chr [1:256] "A1" "E6" "A11" "F4" ...
>  $ sampletype                                         : chr [1:256] "SAMPLE" "SAMPLE" "SAMPLE" "SAMPLE" ...
>  $ ct                                                 : num [1:256] 8.87 12.41 9.57 8.92 8.5 ...
>  $ lodnpx                                             : num [1:256] -9.42 -9.42 -9.34 -9.34 -9.63 ...
>  $ belowlod                                           : logi [1:256] FALSE FALSE FALSE FALSE FALSE FALSE ...
>  $ sampleqc                                           : chr [1:256] "PASS" "PASS" "PASS" "PASS" ...
>  $ assayqc                                            : chr [1:256] "PASS" "PASS" "PASS" "PASS" ...
>  $ softwareversion                                    : chr [1:256] "2.0.2" "2.0.2" "2.0.2" "2.0.2" ...
>  $ softwarename                                       : chr [1:256] "NPX Signature" "NPX Signature" "NPX Signature" "NPX Signature" ...
>  $ reason_excluded                                    : logi [1:256] NA NA NA NA NA NA ...
>  $ excluded                                           : logi [1:256] FALSE FALSE FALSE FALSE FALSE FALSE ...
>  $ plate                                              : Factor w/ 3 levels "GB390725-RB_1",..: 1 1 2 2 3 1 3 2 3 1 ...
>  $ infect.bi.new                                      : num [1:256] 0 1 0 1 0 1 0 1 1 0 ...
>  $ comp.out                                           : num [1:256] 0 1 1 1 0 0 0 0 0 0 ...

Participant age, sex, and infection status are shown below. As is the final.diagnosis.1 variable that was used to derive the infection status variable, infect.

>                        
>                         level                 Overall      
>   n                                             256        
>   age (mean (SD))                             67.14 (16.21)
>   female (%)            0                       172 (67.2) 
>                         1                        84 (32.8) 
>   plate (%)             GB390725-RB_1            83 (32.4) 
>                         GB390725-RB_2            86 (33.6) 
>                         GB390725-RB_3            87 (34.0) 
>   infect.fct (%)        control                  30 (21.1) 
>                         inter                    44 (31.0) 
>                         case                     68 (47.9) 
>   infect.num (%)        1                        30 (21.1) 
>                         2                        44 (31.0) 
>                         3                        68 (47.9) 
>   infect.bi (%)         0                        74 (52.1) 
>                         1                        68 (47.9) 
>   comp.out (%)          0                        88 (62.0) 
>                         1                        54 (38.0) 
>   infect.bi.new (%)     0                       114 (62.6) 
>                         1                        68 (37.4) 
>   final.diagnosis.1 (%) M/breast                  5 ( 2.0) 
>                         M/colorectal              2 ( 0.8) 
>                         M/haem                    4 ( 1.6) 
>                         M/lung/adeno              8 ( 3.1) 
>                         M/lung/small              1 ( 0.4) 
>                         M/lung/squamous           1 ( 0.4) 
>                         M/lung/unsclc             1 ( 0.4) 
>                         M/lung/x                  3 ( 1.2) 
>                         M/meso/biphasic           1 ( 0.4) 
>                         M/meso/desmoplastic       1 ( 0.4) 
>                         M/meso/epithelioid       12 ( 4.7) 
>                         M/meso/sarcomatoid        6 ( 2.3) 
>                         M/meso/x                  1 ( 0.4) 
>                         M/Mullerian               2 ( 0.8) 
>                         M/oesophageal             2 ( 0.8) 
>                         M/ovarian                 1 ( 0.4) 
>                         M/renal                   2 ( 0.8) 
>                         M/sarcoma                 2 ( 0.8) 
>                         M/skin                    2 ( 0.8) 
>                         M/UGI                     2 ( 0.8) 
>                         X/cardiac/u              14 ( 5.5) 
>                         X/hepatic/u              13 ( 5.1) 
>                         X/infection/bacterial    22 ( 8.6) 
>                         X/infection/CPPE         44 (17.2) 
>                         X/infection/SPE          30 (11.7) 
>                         X/infection/utrue        46 (18.0) 
>                         X/inflam/BAPE            14 ( 5.5) 
>                         X/inflam/viral            1 ( 0.4) 
>                         X/renal/u                13 ( 5.1)
> 
>      ### Summary of continuous variables ###
> 
> strata: Overall
>       n miss p.miss mean sd median p25 p75 min max skew kurt
> age 256    0      0   67 16     70  56  79  18  95 -0.6 -0.2
> 
> =======================================================================================
> 
>      ### Summary of categorical variables ### 
> 
> strata: Overall
>                var   n miss p.miss                 level freq percent
>             female 256    0    0.0                     0  172    67.2
>                                                        1   84    32.8
>                                                                      
>              plate 256    0    0.0         GB390725-RB_1   83    32.4
>                                            GB390725-RB_2   86    33.6
>                                            GB390725-RB_3   87    34.0
>                                                                      
>         infect.fct 256  114   44.5               control   30    21.1
>                                                    inter   44    31.0
>                                                     case   68    47.9
>                                                                      
>         infect.num 256  114   44.5                     1   30    21.1
>                                                        2   44    31.0
>                                                        3   68    47.9
>                                                                      
>          infect.bi 256  114   44.5                     0   74    52.1
>                                                        1   68    47.9
>                                                                      
>           comp.out 256  114   44.5                     0   88    62.0
>                                                        1   54    38.0
>                                                                      
>      infect.bi.new 256   74   28.9                     0  114    62.6
>                                                        1   68    37.4
>                                                                      
>  final.diagnosis.1 256    0    0.0              M/breast    5     2.0
>                                             M/colorectal    2     0.8
>                                                   M/haem    4     1.6
>                                             M/lung/adeno    8     3.1
>                                             M/lung/small    1     0.4
>                                          M/lung/squamous    1     0.4
>                                            M/lung/unsclc    1     0.4
>                                                 M/lung/x    3     1.2
>                                          M/meso/biphasic    1     0.4
>                                      M/meso/desmoplastic    1     0.4
>                                       M/meso/epithelioid   12     4.7
>                                       M/meso/sarcomatoid    6     2.3
>                                                 M/meso/x    1     0.4
>                                              M/Mullerian    2     0.8
>                                            M/oesophageal    2     0.8
>                                                M/ovarian    1     0.4
>                                                  M/renal    2     0.8
>                                                M/sarcoma    2     0.8
>                                                   M/skin    2     0.8
>                                                    M/UGI    2     0.8
>                                              X/cardiac/u   14     5.5
>                                              X/hepatic/u   13     5.1
>                                    X/infection/bacterial   22     8.6
>                                         X/infection/CPPE   44    17.2
>                                          X/infection/SPE   30    11.7
>                                        X/infection/utrue   46    18.0
>                                            X/inflam/BAPE   14     5.5
>                                           X/inflam/viral    1     0.4
>                                                X/renal/u   13     5.1
>                                                                      
>  cum.percent
>         67.2
>        100.0
>             
>         32.4
>         66.0
>        100.0
>             
>         21.1
>         52.1
>        100.0
>             
>         21.1
>         52.1
>        100.0
>             
>         52.1
>        100.0
>             
>         62.0
>        100.0
>             
>         62.6
>        100.0
>             
>          2.0
>          2.7
>          4.3
>          7.4
>          7.8
>          8.2
>          8.6
>          9.8
>         10.2
>         10.5
>         15.2
>         17.6
>         18.0
>         18.8
>         19.5
>         19.9
>         20.7
>         21.5
>         22.3
>         23.0
>         28.5
>         33.6
>         42.2
>         59.4
>         71.1
>         89.1
>         94.5
>         94.9
>        100.0
> 

Protein-wide associations

Phenotypic characteristics of participants described in Phenotype information were examined for association pleural protein abundances (Pleural proteins)

Models

The formulae of linear models examined are shown in the table below:

number model.name formula n
1 infect.fct proteins ~ infect.fct 142
2 infect.num proteins ~ infect.num 142
3 infect.bi proteins ~ infect.bi 142
4 comp.out proteins ~ comp.out 142
5 infect.bi.new proteins ~ infect.bi.new 182
6 female proteins ~ female 256
7 age proteins ~ age 256
8 infect.fct.plate proteins ~ infect.fct + plate 142
9 infect.num.plate proteins ~ infect.num + plate 142
10 infect.bi.plate proteins ~ infect.bi + plate 142
11 comp.out.plate proteins ~ comp.out + plate 142
12 infect.bi.new.plate proteins ~ infect.bi.new + plate 182
13 female.plate proteins ~ female + plate 256
14 age.plate proteins ~ age + plate 256
15 infect.fct.fulladj proteins ~ infect.fct + female + age + plate 142
16 infect.num.fulladj proteins ~ infect.num + female + age + plate 142
17 infect.bi.fulladj proteins ~ infect.bi + female + age + plate 142
18 comp.out.fulladj proteins ~ comp.out + female + age + plate 142
19 infect.bi.new.fulladj proteins ~ infect.bi.new + female + age + plate 182

QQ plots

> $infect.fct

> 
> $infect.num

> 
> $infect.bi

> 
> $comp.out

> 
> $infect.bi.new

> 
> $female

> 
> $age

> 
> $infect.fct.plate

> 
> $infect.num.plate

> 
> $infect.bi.plate

> 
> $comp.out.plate

> 
> $infect.bi.new.plate

> 
> $female.plate

> 
> $age.plate

> 
> $infect.fct.fulladj

> 
> $infect.num.fulladj

> 
> $infect.bi.fulladj

> 
> $comp.out.fulladj

> 
> $infect.bi.new.fulladj

Volcano plots

> $infect.fct
> NULL
> 
> $infect.num

> 
> $infect.bi

> 
> $comp.out

> 
> $infect.bi.new

> 
> $female

> 
> $age

> 
> $infect.fct.plate
> NULL
> 
> $infect.num.plate

> 
> $infect.bi.plate

> 
> $comp.out.plate

> 
> $infect.bi.new.plate

> 
> $female.plate

> 
> $age.plate

> 
> $infect.fct.fulladj
> NULL
> 
> $infect.num.fulladj

> 
> $infect.bi.fulladj

> 
> $comp.out.fulladj

> 
> $infect.bi.new.fulladj

Hit counts per model

Number of bonferroni (p< 0.05/92) and fdr adjusted (fdr p < 0.05) hits per model

number model.name formula n bonf.sig fdr.sig
1 infect.fct proteins ~ infect.fct 142 36 50
2 infect.num proteins ~ infect.num 142 37 54
3 infect.bi proteins ~ infect.bi 142 36 54
4 comp.out proteins ~ comp.out 142 23 36
5 infect.bi.new proteins ~ infect.bi.new 182 46 66
6 female proteins ~ female 256 2 4
7 age proteins ~ age 256 25 48
8 infect.fct.plate proteins ~ infect.fct + plate 142 36 51
9 infect.num.plate proteins ~ infect.num + plate 142 37 52
10 infect.bi.plate proteins ~ infect.bi + plate 142 35 54
11 comp.out.plate proteins ~ comp.out + plate 142 24 35
12 infect.bi.new.plate proteins ~ infect.bi.new + plate 182 46 66
13 female.plate proteins ~ female + plate 256 2 4
14 age.plate proteins ~ age + plate 256 26 48
15 infect.fct.fulladj proteins ~ infect.fct + female + age + plate 142 32 47
16 infect.num.fulladj proteins ~ infect.num + female + age + plate 142 34 51
17 infect.bi.fulladj proteins ~ infect.bi + female + age + plate 142 30 45
18 comp.out.fulladj proteins ~ comp.out + female + age + plate 142 23 34
19 infect.bi.new.fulladj proteins ~ infect.bi.new + female + age + plate 182 43 56

Top hits

$infect.fct

feature_id uniprot gene f p.value infect.fctinter.estimate infect.fctinter.se infect.fctinter.t infect.fctinter.p.value infect.fctcase.estimate infect.fctcase.se infect.fctcase.t infect.fctcase.p.value n p.adjust
OID00471 P10145 IL8 40.792 1.151406e-14 2.445 0.435 5.618 1.018206e-07 3.638 0.403 9.029 1.286992e-15 142 1.059293e-12
OID00494 P13725 OSM 38.434 5.168685e-14 1.800 0.487 3.694 3.169406e-04 3.820 0.451 8.467 3.197543e-14 142 4.755190e-12
OID00560 P00813 ADA 37.691 8.354244e-14 1.098 0.421 2.610 1.005735e-02 3.124 0.389 8.023 3.863748e-13 142 7.685905e-12
OID00506 O43557 TNFSF14 33.713 1.156989e-12 0.516 0.541 0.953 3.423543e-01 3.438 0.501 6.863 2.048581e-10 142 1.064430e-10
OID00520 P42830 CXCL5 32.810 2.130872e-12 3.163 0.675 4.684 6.611455e-06 5.047 0.625 8.074 2.904586e-13 142 1.960403e-10
OID00532 P10147 CCL3 32.383 2.849321e-12 0.927 0.512 1.810 7.249174e-02 3.400 0.474 7.173 3.992927e-11 142 2.621376e-10
OID00517 Q13478 IL-18R1 31.442 5.430920e-12 0.726 0.274 2.644 9.129161e-03 1.888 0.254 7.428 1.010442e-11 142 4.996446e-10
OID00493 P01583 IL-1 alpha 30.696 9.097134e-12 1.042 0.632 1.649 1.014864e-01 4.056 0.585 6.930 1.443705e-10 142 8.369363e-10
OID00474 P80098 MCP-3 30.081 1.395527e-11 2.053 0.511 4.016 9.629013e-05 3.626 0.473 7.666 2.779917e-12 142 1.283885e-09
OID00547 P15018 LIF 27.822 6.872673e-11 1.768 0.431 4.104 6.900959e-05 2.956 0.399 7.410 1.114735e-11 142 6.322859e-09

$infect.num

feature_id uniprot gene estimate se t p.value n p.adjust
OID00494 P13725 OSM 1.925 0.219 8.792 4.818058e-15 142 4.432613e-13
OID00471 P10145 IL8 1.735 0.198 8.773 5.375617e-15 142 4.945568e-13
OID00560 P00813 ADA 1.624 0.190 8.539 2.041545e-14 142 1.878221e-12
OID00520 P42830 CXCL5 2.438 0.305 7.998 4.296767e-13 142 3.953026e-11
OID00517 Q13478 IL-18R1 0.973 0.124 7.865 8.990771e-13 142 8.271509e-11
OID00474 P80098 MCP-3 1.781 0.230 7.751 1.684507e-12 142 1.549746e-10
OID00532 P10147 CCL3 1.804 0.233 7.742 1.773699e-12 142 1.631803e-10
OID00506 O43557 TNFSF14 1.881 0.250 7.525 5.831190e-12 142 5.364694e-10
OID00493 P01583 IL-1 alpha 2.160 0.288 7.503 6.565723e-12 142 6.040465e-10
OID00547 P15018 LIF 1.439 0.194 7.417 1.045204e-11 142 9.615879e-10

$infect.bi

feature_id uniprot gene estimate se t p.value n p.adjust
OID00506 O43557 TNFSF14 3.132 0.384 8.159 1.750448e-13 142 1.610412e-11
OID00560 P00813 ADA 2.472 0.305 8.114 2.245166e-13 142 2.065553e-11
OID00532 P10147 CCL3 2.849 0.366 7.779 1.449280e-12 142 1.333338e-10
OID00494 P13725 OSM 2.749 0.361 7.615 3.562077e-12 142 3.277111e-10
OID00493 P01583 IL-1 alpha 3.436 0.451 7.613 3.596543e-12 142 3.308820e-10
OID00517 Q13478 IL-18R1 1.456 0.199 7.321 1.758473e-11 142 1.617795e-09
OID00503 P01135 TGF-alpha 1.786 0.254 7.040 7.905369e-11 142 7.272939e-09
OID00485 Q16552 IL-17A 3.610 0.556 6.498 1.325538e-09 142 1.219495e-07
OID00480 P01137 LAP TGF-beta-1 0.909 0.140 6.481 1.446752e-09 142 1.331012e-07
OID00471 P10145 IL8 2.184 0.341 6.408 2.095754e-09 142 1.928094e-07

$comp.out

feature_id uniprot gene estimate se t p.value n p.adjust
OID00520 P42830 CXCL5 3.434 0.521 6.597 7.974417e-10 142 7.336464e-08
OID00494 P13725 OSM 2.389 0.393 6.078 1.092128e-08 142 1.004758e-06
OID00532 P10147 CCL3 2.346 0.405 5.791 4.409204e-08 142 4.056468e-06
OID00485 Q16552 IL-17A 3.366 0.587 5.735 5.771884e-08 142 5.310133e-06
OID00517 Q13478 IL-18R1 1.236 0.217 5.702 6.741430e-08 142 6.202116e-06
OID00503 P01135 TGF-alpha 1.558 0.274 5.690 7.136774e-08 142 6.565832e-06
OID00472 P15692 VEGFA 0.760 0.137 5.548 1.397401e-07 142 1.285609e-05
OID00471 P10145 IL8 1.997 0.361 5.525 1.554160e-07 142 1.429828e-05
OID00493 P01583 IL-1 alpha 2.761 0.501 5.516 1.622447e-07 142 1.492651e-05
OID00506 O43557 TNFSF14 2.348 0.437 5.374 3.135013e-07 142 2.884212e-05

$infect.bi.new

feature_id uniprot gene estimate se t p.value n p.adjust
OID00560 P00813 ADA 2.997 0.274 10.929 1.194356e-21 182 1.098807e-19
OID00506 O43557 TNFSF14 3.482 0.320 10.884 1.604814e-21 182 1.476429e-19
OID00494 P13725 OSM 3.487 0.324 10.751 3.876123e-21 182 3.566033e-19
OID00532 P10147 CCL3 3.118 0.304 10.265 9.387083e-20 182 8.636117e-18
OID00493 P01583 IL-1 alpha 3.770 0.373 10.118 2.453722e-19 182 2.257424e-17
OID00517 Q13478 IL-18R1 1.716 0.174 9.848 1.412641e-18 182 1.299630e-16
OID00474 P80098 MCP-3 3.362 0.361 9.310 4.445174e-17 182 4.089560e-15
OID00503 P01135 TGF-alpha 1.917 0.210 9.124 1.443610e-16 182 1.328121e-14
OID00520 P42830 CXCL5 4.032 0.449 8.989 3.380271e-16 182 3.109850e-14
OID00485 Q16552 IL-17A 4.133 0.465 8.884 6.515655e-16 182 5.994403e-14

$female

feature_id uniprot gene estimate se t p.value n p.adjust
OID00512 Q9NSA1 FGF-21 1.092 0.302 3.610 3.685466e-04 256 3.390629e-02
OID00534 P80162 CXCL6 0.650 0.181 3.597 3.870928e-04 256 3.561253e-02
OID00481 P00749 uPA -0.244 0.075 -3.245 1.331245e-03 256 1.224745e-01
OID00480 P01137 LAP TGF-beta-1 -0.379 0.119 -3.171 1.705441e-03 256 1.569005e-01
OID00554 P20783 NT-3 -0.585 0.200 -2.925 3.760519e-03 256 3.459677e-01
OID00476 Q9H5V8 CDCP1 -0.398 0.142 -2.798 5.536915e-03 256 5.093962e-01
OID00472 P15692 VEGFA -0.338 0.123 -2.738 6.612371e-03 256 6.083381e-01
OID00513 Q99731 CCL19 0.529 0.198 2.670 8.069177e-03 256 7.423643e-01
OID00530 P55773 CCL23 0.252 0.099 2.554 1.124655e-02 256 1.000000e+00
OID00528 P22301 IL10 0.456 0.188 2.428 1.585718e-02 256 1.000000e+00

$age

feature_id uniprot gene estimate se t p.value n p.adjust
OID00539 Q9NRJ3 CCL28 0.017 0.002 6.917 3.729325e-11 256 3.430979e-09
OID00551 O15444 CCL25 0.030 0.004 6.830 6.245990e-11 256 5.746311e-09
OID00521 O14788 TRANCE -0.043 0.006 -6.775 8.617535e-11 256 7.928132e-09
OID00524 Q13007 IL-24 -0.039 0.006 -6.620 2.126886e-10 256 1.956735e-08
OID00491 P28325 CST5 0.025 0.004 6.314 1.203104e-09 256 1.106856e-07
OID00485 Q16552 IL-17A -0.078 0.013 -6.131 3.319032e-09 256 3.053509e-07
OID00537 Q9NYY1 IL-20 -0.011 0.002 -6.066 4.737243e-09 256 4.358264e-07
OID00493 P01583 IL-1 alpha -0.056 0.010 -5.579 6.198957e-08 256 5.703041e-06
OID00506 O43557 TNFSF14 -0.051 0.009 -5.547 7.273614e-08 256 6.691725e-06
OID00497 Q969D9 TSLP -0.036 0.007 -5.519 8.415167e-08 256 7.741953e-06

$infect.fct.plate

feature_id uniprot gene f p.value infect.fctinter.estimate infect.fctinter.se infect.fctinter.t infect.fctinter.p.value infect.fctcase.estimate infect.fctcase.se infect.fctcase.t infect.fctcase.p.value n p.adjust
OID00471 P10145 IL8 40.441 1.574265e-14 2.443 0.438 5.579 1.247352e-07 3.645 0.405 8.990 1.772363e-15 142 1.448324e-12
OID00494 P13725 OSM 37.957 7.643807e-14 1.807 0.488 3.704 3.064442e-04 3.807 0.452 8.425 4.379990e-14 142 7.032303e-12
OID00560 P00813 ADA 37.055 1.369683e-13 1.102 0.422 2.611 1.004131e-02 3.114 0.391 7.966 5.662214e-13 142 1.260108e-11
OID00506 O43557 TNFSF14 33.071 1.910030e-12 0.516 0.543 0.951 3.433746e-01 3.421 0.503 6.804 2.904822e-10 142 1.757228e-10
OID00520 P42830 CXCL5 32.275 3.273649e-12 3.167 0.680 4.658 7.476900e-06 5.043 0.630 8.010 4.449227e-13 142 3.011757e-10
OID00532 P10147 CCL3 31.846 4.384685e-12 0.924 0.513 1.800 7.407088e-02 3.383 0.475 7.117 5.612528e-11 142 4.033910e-10
OID00517 Q13478 IL-18R1 30.848 8.697417e-12 0.726 0.276 2.627 9.589298e-03 1.884 0.256 7.362 1.519183e-11 142 8.001624e-10
OID00547 P15018 LIF 30.205 1.357330e-11 1.772 0.419 4.229 4.266656e-05 2.994 0.388 7.715 2.250523e-12 142 1.248744e-09
OID00493 P01583 IL-1 alpha 30.104 1.455512e-11 1.042 0.635 1.641 1.031482e-01 4.038 0.588 6.868 2.074110e-10 142 1.339071e-09
OID00474 P80098 MCP-3 29.916 1.658490e-11 2.056 0.514 4.002 1.023049e-04 3.637 0.476 7.645 3.302405e-12 142 1.525811e-09

$infect.num.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00471 P10145 IL8 1.740 0.199 8.741 7.007198e-15 142 6.446622e-13
OID00494 P13725 OSM 1.916 0.219 8.739 7.097413e-15 142 6.529620e-13
OID00560 P00813 ADA 1.618 0.191 8.472 3.221973e-14 142 2.964215e-12
OID00520 P42830 CXCL5 2.435 0.307 7.930 6.671000e-13 142 6.137320e-11
OID00517 Q13478 IL-18R1 0.971 0.125 7.792 1.430294e-12 142 1.315871e-10
OID00547 P15018 LIF 1.460 0.189 7.736 1.945890e-12 142 1.790219e-10
OID00474 P80098 MCP-3 1.787 0.231 7.731 1.997804e-12 142 1.837979e-10
OID00532 P10147 CCL3 1.794 0.234 7.679 2.655369e-12 142 2.442940e-10
OID00506 O43557 TNFSF14 1.870 0.251 7.456 8.918821e-12 142 8.205315e-10
OID00493 P01583 IL-1 alpha 2.150 0.289 7.433 1.010247e-11 142 9.294273e-10

$infect.bi.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00506 O43557 TNFSF14 3.114 0.385 8.080 2.911567e-13 142 2.678641e-11
OID00560 P00813 ADA 2.459 0.306 8.036 3.721765e-13 142 3.424024e-11
OID00532 P10147 CCL3 2.834 0.367 7.713 2.209400e-12 142 2.032648e-10
OID00494 P13725 OSM 2.732 0.362 7.546 5.487093e-12 142 5.048126e-10
OID00493 P01583 IL-1 alpha 3.419 0.454 7.538 5.735502e-12 142 5.276662e-10
OID00517 Q13478 IL-18R1 1.453 0.200 7.249 2.721175e-11 142 2.503481e-09
OID00503 P01135 TGF-alpha 1.769 0.253 6.982 1.119821e-10 142 1.030235e-08
OID00485 Q16552 IL-17A 3.591 0.553 6.489 1.434744e-09 142 1.319964e-07
OID00480 P01137 LAP TGF-beta-1 0.909 0.141 6.438 1.861760e-09 142 1.712819e-07
OID00471 P10145 IL8 2.193 0.343 6.391 2.360470e-09 142 2.171632e-07

$comp.out.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00520 P42830 CXCL5 3.444 0.526 6.543 1.088756e-09 142 1.001656e-07
OID00494 P13725 OSM 2.372 0.396 5.991 1.718156e-08 142 1.580704e-06
OID00532 P10147 CCL3 2.315 0.409 5.663 8.313001e-08 142 7.647961e-06
OID00517 Q13478 IL-18R1 1.234 0.219 5.626 9.904845e-08 142 9.112458e-06
OID00485 Q16552 IL-17A 3.307 0.589 5.616 1.037101e-07 142 9.541333e-06
OID00503 P01135 TGF-alpha 1.525 0.275 5.538 1.492591e-07 142 1.373183e-05
OID00471 P10145 IL8 2.021 0.365 5.538 1.495283e-07 142 1.375660e-05
OID00472 P15692 VEGFA 0.765 0.138 5.520 1.622837e-07 142 1.493010e-05
OID00493 P01583 IL-1 alpha 2.730 0.506 5.400 2.835860e-07 142 2.608991e-05
OID00474 P80098 MCP-3 2.207 0.409 5.399 2.846556e-07 142 2.618831e-05

$infect.bi.new.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00560 P00813 ADA 2.994 0.276 10.849 2.265079e-21 182 2.083873e-19
OID00506 O43557 TNFSF14 3.467 0.321 10.789 3.357381e-21 182 3.088790e-19
OID00494 P13725 OSM 3.484 0.326 10.687 6.576807e-21 182 6.050662e-19
OID00532 P10147 CCL3 3.094 0.304 10.163 2.011831e-19 182 1.850885e-17
OID00493 P01583 IL-1 alpha 3.749 0.374 10.014 5.266396e-19 182 4.845084e-17
OID00517 Q13478 IL-18R1 1.715 0.176 9.770 2.534297e-18 182 2.331553e-16
OID00474 P80098 MCP-3 3.372 0.363 9.281 5.741965e-17 182 5.282607e-15
OID00503 P01135 TGF-alpha 1.903 0.210 9.045 2.532326e-16 182 2.329740e-14
OID00520 P42830 CXCL5 4.027 0.452 8.914 5.751981e-16 182 5.291823e-14
OID00485 Q16552 IL-17A 4.081 0.464 8.792 1.234450e-15 182 1.135694e-13

$female.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00512 Q9NSA1 FGF-21 1.106 0.305 3.625 3.490570e-04 256 3.211325e-02
OID00534 P80162 CXCL6 0.650 0.182 3.567 4.314778e-04 256 3.969596e-02
OID00481 P00749 uPA -0.255 0.076 -3.363 8.905882e-04 256 8.193412e-02
OID00480 P01137 LAP TGF-beta-1 -0.388 0.120 -3.227 1.418667e-03 256 1.305174e-01
OID00554 P20783 NT-3 -0.568 0.202 -2.820 5.177238e-03 256 4.763059e-01
OID00476 Q9H5V8 CDCP1 -0.401 0.143 -2.806 5.409842e-03 256 4.977054e-01
OID00472 P15692 VEGFA -0.343 0.124 -2.759 6.229267e-03 256 5.730926e-01
OID00513 Q99731 CCL19 0.537 0.200 2.689 7.648306e-03 256 7.036442e-01
OID00528 P22301 IL10 0.483 0.187 2.582 1.037418e-02 256 9.544243e-01
OID00530 P55773 CCL23 0.248 0.099 2.492 1.335111e-02 256 1.000000e+00

$age.plate

feature_id uniprot gene estimate se t p.value n p.adjust
OID00539 Q9NRJ3 CCL28 0.018 0.002 7.247 5.191004e-12 256 4.775724e-10
OID00521 O14788 TRANCE -0.044 0.006 -6.972 2.733985e-11 256 2.515266e-09
OID00551 O15444 CCL25 0.031 0.004 6.915 3.839852e-11 256 3.532664e-09
OID00524 Q13007 IL-24 -0.039 0.006 -6.478 4.834237e-10 256 4.447498e-08
OID00491 P28325 CST5 0.025 0.004 6.344 1.032973e-09 256 9.503350e-08
OID00485 Q16552 IL-17A -0.078 0.013 -6.109 3.777703e-09 256 3.475487e-07
OID00537 Q9NYY1 IL-20 -0.011 0.002 -6.055 5.061662e-09 256 4.656729e-07
OID00493 P01583 IL-1 alpha -0.057 0.010 -5.685 3.617836e-08 256 3.328409e-06
OID00506 O43557 TNFSF14 -0.052 0.009 -5.636 4.638017e-08 256 4.266976e-06
OID00497 Q969D9 TSLP -0.037 0.007 -5.569 6.559671e-08 256 6.034897e-06

$infect.fct.fulladj

feature_id uniprot gene f p.value infect.fctinter.estimate infect.fctinter.se infect.fctinter.t infect.fctinter.p.value infect.fctcase.estimate infect.fctcase.se infect.fctcase.t infect.fctcase.p.value n p.adjust
OID00471 P10145 IL8 36.097 2.767321e-13 2.434 0.440 5.538 1.541841e-07 3.553 0.418 8.495 3.201632e-14 142 2.545936e-11
OID00494 P13725 OSM 32.087 3.974159e-12 1.778 0.476 3.732 2.791033e-04 3.556 0.453 7.843 1.191209e-12 142 3.656227e-10
OID00560 P00813 ADA 30.753 9.878257e-12 1.062 0.421 2.522 1.283472e-02 2.938 0.401 7.333 1.875102e-11 142 9.087997e-10
OID00520 P42830 CXCL5 29.693 2.053599e-11 3.176 0.686 4.629 8.545620e-06 5.027 0.653 7.698 2.618073e-12 142 1.889311e-09
OID00506 O43557 TNFSF14 27.560 9.187858e-11 0.493 0.535 0.922 3.579182e-01 3.191 0.509 6.269 4.557791e-09 142 8.452830e-09
OID00532 P10147 CCL3 27.290 1.113156e-10 0.915 0.513 1.782 7.696916e-02 3.256 0.489 6.664 6.200890e-10 142 1.024104e-08
OID00547 P15018 LIF 26.362 2.163028e-10 1.767 0.409 4.323 2.969540e-05 2.820 0.389 7.251 2.896449e-11 142 1.989986e-08
OID00517 Q13478 IL-18R1 26.066 2.676114e-10 0.717 0.275 2.607 1.017389e-02 1.794 0.262 6.852 2.350786e-10 142 2.462025e-08
OID00493 P01583 IL-1 alpha 25.604 3.737053e-10 1.039 0.620 1.677 9.577334e-02 3.793 0.590 6.433 2.004019e-09 142 3.438089e-08
OID00474 P80098 MCP-3 25.214 4.961115e-10 2.026 0.509 3.978 1.127320e-04 3.427 0.485 7.069 7.581914e-11 142 4.564226e-08

$infect.num.fulladj

feature_id uniprot gene estimate se t p.value n p.adjust
OID00471 P10145 IL8 1.696 0.207 8.204 1.568546e-13 142 1.443063e-11
OID00494 P13725 OSM 1.778 0.221 8.041 3.878951e-13 142 3.568635e-11
OID00560 P00813 ADA 1.519 0.196 7.731 2.119135e-12 142 1.949604e-10
OID00520 P42830 CXCL5 2.432 0.320 7.594 4.470516e-12 142 4.112875e-10
OID00517 Q13478 IL-18R1 0.919 0.128 7.181 4.109670e-11 142 3.780896e-09
OID00547 P15018 LIF 1.366 0.191 7.170 4.343117e-11 142 3.995668e-09
OID00532 P10147 CCL3 1.716 0.241 7.119 5.679747e-11 142 5.225368e-09
OID00474 P80098 MCP-3 1.675 0.237 7.069 7.430862e-11 142 6.836393e-09
OID00493 P01583 IL-1 alpha 2.002 0.291 6.885 1.947416e-10 142 1.791622e-08
OID00506 O43557 TNFSF14 1.731 0.254 6.804 2.962744e-10 142 2.725724e-08

$infect.bi.fulladj

feature_id uniprot gene estimate se t p.value n p.adjust
OID00506 O43557 TNFSF14 2.892 0.392 7.371 1.491075e-11 142 1.371789e-09
OID00560 P00813 ADA 2.295 0.315 7.284 2.372586e-11 142 2.182779e-09
OID00532 P10147 CCL3 2.702 0.380 7.113 5.878419e-11 142 5.408146e-09
OID00493 P01583 IL-1 alpha 3.164 0.458 6.911 1.699493e-10 142 1.563533e-08
OID00494 P13725 OSM 2.479 0.366 6.774 3.457751e-10 142 3.181131e-08
OID00517 Q13478 IL-18R1 1.359 0.206 6.594 8.699806e-10 142 8.003822e-08
OID00503 P01135 TGF-alpha 1.642 0.257 6.391 2.432245e-09 142 2.237666e-07
OID00485 Q16552 IL-17A 3.332 0.559 5.963 2.019881e-08 142 1.858290e-06
OID00471 P10145 IL8 2.079 0.356 5.839 3.684152e-08 142 3.389420e-06
OID00520 P42830 CXCL5 3.104 0.540 5.745 5.755156e-08 142 5.294744e-06

$comp.out.fulladj

feature_id uniprot gene estimate se t p.value n p.adjust
OID00520 P42830 CXCL5 3.374 0.529 6.383 2.532417e-09 142 2.329824e-07
OID00494 P13725 OSM 2.226 0.378 5.889 2.887224e-08 142 2.656246e-06
OID00485 Q16552 IL-17A 3.125 0.568 5.503 1.798391e-07 142 1.654520e-05
OID00532 P10147 CCL3 2.211 0.403 5.491 1.899536e-07 142 1.747574e-05
OID00517 Q13478 IL-18R1 1.172 0.215 5.460 2.191901e-07 142 2.016549e-05
OID00503 P01135 TGF-alpha 1.438 0.266 5.406 2.812676e-07 142 2.587662e-05
OID00472 P15692 VEGFA 0.731 0.136 5.378 3.196154e-07 142 2.940461e-05
OID00471 P10145 IL8 1.941 0.362 5.363 3.415542e-07 142 3.142298e-05
OID00493 P01583 IL-1 alpha 2.558 0.485 5.272 5.163680e-07 142 4.750586e-05
OID00474 P80098 MCP-3 2.085 0.399 5.232 6.182904e-07 142 5.688272e-05

$infect.bi.new.fulladj

feature_id uniprot gene estimate se t p.value n p.adjust
OID00560 P00813 ADA 2.842 0.284 10.014 5.779650e-19 182 5.317278e-17
OID00506 O43557 TNFSF14 3.251 0.326 9.972 7.538854e-19 182 6.935745e-17
OID00494 P13725 OSM 3.246 0.331 9.810 2.136238e-18 182 1.965339e-16
OID00532 P10147 CCL3 2.974 0.314 9.459 2.002393e-17 182 1.842202e-15
OID00493 P01583 IL-1 alpha 3.483 0.378 9.212 9.526684e-17 182 8.764549e-15
OID00517 Q13478 IL-18R1 1.623 0.180 8.998 3.640417e-16 182 3.349183e-14
OID00474 P80098 MCP-3 3.220 0.375 8.582 4.761817e-15 182 4.380871e-13
OID00520 P42830 CXCL5 4.009 0.469 8.543 6.062950e-15 182 5.577914e-13
OID00503 P01135 TGF-alpha 1.757 0.213 8.261 3.363260e-14 182 3.094199e-12
OID00471 P10145 IL8 2.669 0.324 8.240 3.814632e-14 182 3.509461e-12

Gene-annotated volcano plots

> $infect.num.fulladj

> 
> $infect.bi.fulladj

> 
> $comp.out.fulladj

> 
> $infect.bi.new.fulladj